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122583 commits

Author SHA1 Message Date
Navid Afkhami
32cdced051
gnu: Add r-oompabase.
* gnu/packages/cran.scm (r-oompabase): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 10:29:26 +02:00
Navid Afkhami
48d90820e4
gnu: Add r-oompadata.
* gnu/packages/cran.scm (r-oompadata): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 10:25:50 +02:00
Navid Afkhami
cf941786ee
gnu: Add r-mousegastrulationdata.
* gnu/packages/bioconductor.scm (r-mousegastrulationdata): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 10:19:53 +02:00
Navid Afkhami
aa47077a8b
gnu: Add r-bumpymatrix.
* gnu/packages/bioconductor.scm (r-bumpymatrix): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 10:17:27 +02:00
Navid Afkhami
0b0e050415
gnu: Add r-msigdb.
* gnu/packages/bioconductor.scm (r-msigdb): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 10:06:37 +02:00
Navid Afkhami
aaf261cc8c
gnu: Add r-earlywarnings.
* gnu/packages/cran.scm (r-earlywarnings): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 10:01:17 +02:00
Navid Afkhami
432cf5b449
gnu: Add r-tgp.
* gnu/packages/cran.scm (r-tgp): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 09:58:06 +02:00
Navid Afkhami
2dc030f38f
gnu: Add r-maptree.
* gnu/packages/cran.scm (r-maptree): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 09:54:46 +02:00
Navid Afkhami
dd14ee0676
gnu: Add python-scdamandtools.
* gnu/packages/bioinformatics.scm (python-scdamandtools): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-28 09:50:08 +02:00
Leo Famulari
0aa74bebe3
gnu: linux-libre 6.1: Update to 6.1.47.
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.47.
(linux-libre-6.1-pristine-source): Update hash.
2023-07-23 22:26:00 -04:00
Leo Famulari
96d89018a0
gnu: linux-libre: Update to 6.4.12.
* gnu/packages/linux.scm (linux-libre-6.4-version): Update to 6.4.12.
(linux-libre-6.4-pristine-source): Update hash.
2023-07-23 22:26:00 -04:00
Tobias Geerinckx-Rice
5a2c3352d8
Revert "gnu: system: Add home-directory-permissions field to <user-account>."
This reverts commit e9a5eebc78, which
as far as I can tell breaks system roll-backs thusly:

[...]
In gnu/build/accounts.scm:
   239:27  3 (_ #<<password-entry> name: "root" password: "x" uid: 0 gid: 0 real-name: "System >)
In unknown file:
           2 (string-join ("root" "x" "0" "0" "System administrator" "/root" #t) ":" #<undefined>)
In ice-9/boot-9.scm:
  1685:16  1 (raise-exception _ #:continuable? _)
  1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
In procedure string-append: Wrong type (expecting string): #t
2023-08-20 02:00:00 +02:00
Greg Hogan
37cca1d87e
gnu: vbz-compression: Update to 1.0.3.
* gnu/packages/bioinformatics.scm (vbz-compression): Update to 1.0.3.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:16:45 +01:00
Greg Hogan
1ae56be99e
gnu: spdlog: Fix tests.
* gnu/packages/patches/spdlog-fix-tests.patch: New file.
* gnu/local.mk: Add it.
* gnu/packages/logging.scm (spdlog)[source]: Use patch.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:16:45 +01:00
Greg Hogan
68b3d71806
gnu: catch2: Update to 3.4.0.
* gnu/packages/check.scm (catch2): Update to 3.4.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:16:44 +01:00
Cayetano Santos
e7c7efc296
gnu: emacs-corfu-doc-terminal: Update to 0.9.
* gnu/packages/emacs-xyz.scm (emacs-corfu-doc-terminal): Update to 0.9.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:11:30 +01:00
Cayetano Santos
35421248b1
gnu: emacs-gptel: Update to 0.4.0.
* gnu/packages/emacs-xyz.scm (emacs-gptel): Update to 0.4.0.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:11:07 +01:00
Greg Hogan
6482f61a0c
gnu: python-graph-tool: Update to 2.57.
* gnu/packages/graph.scm (python-graph-tool): Update to 2.57.
[propagated-inputs]: Add python-zstandard.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:10:23 +01:00
Andy Tai
be2786144c
gnu: gemmlowp: Update to 0.1-1.08e4bb3.
* gnu/packages/machine-learning.scm (gemmlowp): Update to 0.1-1.08e4bb3.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-27 19:05:57 +01:00
Andreas Enge
8b4a248fc4
Update tex team.
* etc/teams.scm.in: Add gnu/packages/texlive.scm to the files and Andreas
Enge to the members of the tex team.
2023-08-27 12:26:49 +02:00
Hilton Chain
5856e185a3
gnu: Add tree-sitter-cmake.
* gnu/packages/tree-sitter.scm (tree-sitter-cmake): New variable.
2023-08-27 12:11:04 +08:00
Hilton Chain
493e9c2f54
gnu: phantomsocks: Update to 0.0.0-20230811053544-53b995bdab83.
* gnu/packages/networking.scm (phantomsocks): Update to
0.0.0-20230811053544-53b995bdab83.
[propagated-inputs]: Move go-github-com-google-gopacket and
go-github-com-macronut-go-tproxy to...
[inputs]: ...here.
2023-08-27 12:08:00 +08:00
Hilton Chain
0ba7debb02
gnu: picard: Update to 2.9.1.
* gnu/packages/music.scm (picard): Update to 2.9.1.
[uri]: Switch mirror.
[#:phases]: Add phase 'set-HOME.
Remove phase 'delete-failing-test.
2023-08-27 12:05:16 +08:00
Piotr Kwiecinski
e9bea73e2d
gnu: emacs-orderless: Update to 1.0.
* gnu/packages/emacs-xyz.scm (emacs-orderless): Update to 1.0, previously used
commit was pointing to 0.8.

Signed-off-by: Hilton Chain <hako@ultrarare.space>
2023-08-27 11:41:11 +08:00
Fabio Natali
262efbf9b1
gnu: emacs-hide-mode-line: Update to 1.0.3.
* gnu/packages/emacs-xyz.scm (emacs-hide-mode-line): Update to 1.0.3.

Signed-off-by: Hilton Chain <hako@ultrarare.space>
2023-08-27 11:39:53 +08:00
Cayetano Santos
5476f79e41
gnu: emacs-helpful: Update to 0.21.
* gnu/packages/emacs-xyz.scm (emacs-helpful): Update to 0.21.

Signed-off-by: Hilton Chain <hako@ultrarare.space>
2023-08-27 11:33:58 +08:00
Lu Hui
28fdf6cc16
gnu: libsigrokdecode: Update to 0.5.3-0.e6962b3, fix build.
* gnu/packages/electronics.scm (libsigrokdecode): Update to 0.5.3-0.e6962b3.
[source]: Use git-fetch.  Remove patches.
[native-inputs]: Add libtool.
[arguments]<#:phases>: Remove bootstrap phase.
* gnu/packages/patches/libsigrokdecode-python3.9-fix.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Unregister it.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-27 10:19:34 +08:00
Maxim Cournoyer
1dce887776
gnu-maintenance: Consider Qt source tarballs as "release files".
* guix/gnu-maintenance.scm (release-file?): Use positive logic in doc.
Add a special case for Qt source archives.
* tests/gnu-maintenance.scm ("release-file?"): Update test.
2023-08-26 11:38:56 -04:00
Maxim Cournoyer
bdaef69556
gnu-maintenance: Allow mirror URLs to fallback to the generic HTML updater.
* guix/gnu-maintenance.scm (http-url?): Extract from html-updatable-package?,
modify to return the HTTP URL, and support the mirror:// scheme.
(%disallowed-hosting-sites): New variable, extracted from
html-updatable-package.
(html-updatable-package?): Rewrite a mirror:// URL to an HTTP or HTTPS one.
* guix/download.scm (%mirrors): Update comment.
2023-08-26 11:38:56 -04:00
Maxim Cournoyer
6953fb9241
gnu-maintenance: Add support to rewrite version in URL path.
Fixes <https://issues.guix.gnu.org/64015>.
Fixes <https://issues.guix.gnu.org/65304>.

Previously, the generic HTML updater would only look for the list of files
found at the parent of its current source URL, ignoring that the URL may embed
the version elsewhere in its path.  This could cause 'guix refresh' to report
no updates available, while in fact there were, such as for 'libuv'.

* guix/gnu-maintenance.scm (strip-trailing-slash): New procedure.
(%version-rx): New variable.
(rewrite-url): New procedure.
(import-html-release): New rewrite-url? argument.  When true, use the above
procedure.
(import-html-updatable-release): Call import-html-release with #:rewrite-url
set to #t.
* tests/gnu-maintenance.scm ("rewrite-url, to-version specified")
("rewrite-url, without to-version"): New tests.
2023-08-26 11:38:56 -04:00
Maxim Cournoyer
6fb8cc312d
gnu-maintenance: Extract 'canonicalize-url' from 'import-html-release'.
* guix/gnu-maintenance.scm
(canonicalize-url): New procedure, extracted from...
(import-html-release): ... here.  Use it.  Rename inner PACKAGE variable to
NAME, to explicit it is a string and not a package object.
2023-08-26 11:38:56 -04:00
Maxim Cournoyer
2654232660
gnu-maintenance: Document nested procedures in 'import-html-release'.
* guix/gnu-maintenance.scm (import-html-release): Add docstring to the
'file->signature/guess' and 'url->release' nested procedures.
2023-08-26 11:38:56 -04:00
Maxim Cournoyer
c6b5eeac92
gnu-maintenance: Accept package object in 'import-html-release' procedure.
This is in preparation for a new URL rewriting feature, which will need to
have the current version information available.

* guix/gnu-maintenance.scm (import-html-release): Update doc.  Adjust default
value of the DIRECTORY argument.  Bind PACKAGE in lexical scope so that its
value there is unchanged.
(import-savannah-release, import-kernel.org-release)
(import-html-updatable-release): Adjust accordingly.
2023-08-26 11:38:56 -04:00
Maxim Cournoyer
a5e67dec2a
gnu-maintenance: Fix indentation.
* guix/gnu-maintenance.scm: Re-indent file.
2023-08-26 11:38:55 -04:00
Maxim Cournoyer
f6cfc993ac
gnu-maintenance: Extract url->links procedure.
* guix/gnu-maintenance.scm (url->links): New procedure.
(import-html-release): Use it.
2023-08-26 11:38:55 -04:00
Maxim Cournoyer
610d0e30e0
gnu-maintenance: Fix docstring.
* guix/gnu-maintenance.scm (import-kernel.org-release): Fix docstring.
2023-08-26 11:38:55 -04:00
Maxim Cournoyer
4110cc4f75
gnu-maintenance: Make base-url argument of import-html-release required.
It doesn't make sense to have it default to something like
"https://kernel.org/pub"; it should always be provided explicitly.

* guix/gnu-maintenance.scm (import-html-release) <#:base-url>: Turn keyword
argument into a positional argument.  Update doc.
* guix/gnu-maintenance.scm (import-savannah-release): Adjust call accordingly.
(import-kernel.org-release): Likewise.
(import-html-updatable-release): Likewise.
2023-08-26 11:38:55 -04:00
fanquake
cfe55b220a
gnu: libmtp: Update to 1.1.21.
* gnu/packages/libusb.scm (libmtp): Update to 1.1.21.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-26 12:44:03 +01:00
flabbergasted
bdea9adc86
gnu: neomutt: Update to 20230517.
* gnu/packages/mail.scm (neomutt): Update to 20230517.

Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-26 12:36:28 +01:00
Christopher Baines
5ac265c9f0
gnu: guix-build-coordinator: Update to 0-87.06a4469.
* gnu/packages/package-management.scm (guix-build-coordinator): Update to
0-87.06a4469.
2023-08-26 12:21:41 +01:00
Christopher Baines
d823ed25d5
services: nar-herder: Specify a working directory.
Mostly so that core dumps end up here.

* gnu/services/guix.scm (nar-herder-shepherd-services): Specify a working
directory.
2023-08-26 12:19:14 +01:00
Christopher Baines
82b5e89d78
services: guix-data-service: Specify a working directory.
Mostly so that core dumps end up here.

* gnu/services/guix.scm (guix-data-service-shepherd-services): Specify a
working directory.
2023-08-26 12:18:52 +01:00
Christopher Baines
aba7c73d04
services: guix-build-coordinator: Specify a working directory.
Mostly so that core dumps end up here.

* gnu/services/guix.scm (guix-build-coordinator-shepherd-services): Specify a
working directory.
2023-08-26 12:18:08 +01:00
Zheng Junjie
eeb71d778f
gnu: pkgconf: Update to 2.0.2.
* gnu/packages/pkg-config.scm (pkgconf): Update to 2.0.2.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-26 11:30:27 +08:00
kiasoc5
98f9a35f53
gnu: xsecurelock: Update to 1.8.0.
* gnu/packages/xdisorg.scm (xsecurelock): Update to 1.8.0.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-26 11:30:27 +08:00
kiasoc5
428327e6be
gnu: ydotool: Update to 1.0.4.
* gnu/packages/xdisorg.scm (ydotool): Update to 1.0.4.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-26 11:30:27 +08:00
kiasoc5
92f301ffd8
gnu: xlockmore: Update to 5.72.
* gnu/packages/xdisorg.scm (xlockmore): Update to 5.72.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-26 11:30:16 +08:00
kiasoc5
9f1a39ac3d
gnu: autorandr: Update to 1.14.
* gnu/packages/xdisorg.scm (autorandr): Update to 1.14.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-26 11:22:33 +08:00
Bruno Victal
c135d9747e
gnu: mympd: Update to 11.0.4.
* gnu/packages/mpd.scm (mympd): Update to 11.0.4.

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2023-08-26 11:16:57 +08:00
宋文武
10d4923691
gnu: rizin: Update to 0.6.1.
* gnu/packages/engineering.scm (rizin): Update to 0.6.1.
[arguments]<#:phases>: Enable a now passing test (analysis_var).
2023-08-26 11:15:29 +08:00